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Hannes Stark @hannes-stark.bsky.social · 3d

Tomorrow we have a reading group session with @nscorley and @SimMat20 about "Accelerating Biomolecular Modeling with AtomWorks and RF3" www.biorxiv.org/content/10.1...

We will also discuss how to close the gap between AF3 and its open source replications!

portal.valencelabs.com/starklyspeak...

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Hannes Stark @hannes-stark.bsky.social · Aug 3

Tomorrow we discuss diffusion models for sampling unnormalized densities "Adjoint Sampling: Highly Scalable Diffusion Samplers via Adjoint Matching"
arxiv.org/abs/2504.11713

Join us on zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...

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Hannes Stark @hannes-stark.bsky.social · Jul 21

In 1h we discuss "Predicting cellular responses to perturbation across diverse contexts with State" in the reading group with the author Abhinav Adduri! www.biorxiv.org/content/10.1...

Join us on zoom at 9am PT / 12pm ET: portal.valencelabs.com/starklyspeak...

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Hannes Stark @hannes-stark.bsky.social · Jun 29

Starkly Speaking tomorrow: @bwood_m will present "UMA: A Family of Universal Models for Atoms" ai.meta.com/research/pub...

Join us on Zoom 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...

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Hannes Stark @hannes-stark.bsky.social · Jun 21

Monday Starkly Speaking: we understand a core diffusion model ingredient better - classifier free guidance.

Via "Classifier-Free Guidance: From High-Dimensional Analysis to Generalized Guidance Forms" arxiv.org/abs/2502.07849

On Zoom 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...

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Hannes Stark @hannes-stark.bsky.social · Jun 18

Presentation of Boltz-2 by @pas_saro @GabriCorso @jeremyWohlwend!

Structure models and careful affinity data handling result in an affinity predictor approaching FEP accuracy at 1000x the speed.

www.youtube.com/watch?v=iHDa...

Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction

YouTube video by Valence Labs

www.youtube.com

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Reposted by Hannes Stark

Gabriele Corso @gcorso.bsky.social · Jun 14

Thank you everyone for attending the Boltz-2 Boston, San Francisco and Paris events this week! Given the success of the in-person seminars and the many requests, we are organizing a virtual seminar on Tuesday at 12pm ET / 6pm CET! Sign up here: lu.ma/4bpuwbsr

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Hannes Stark @hannes-stark.bsky.social · Jun 14

On Tue 12pm ET on Zoom: Saro Passaro, Gabriele Corso, Jeremy Wohlwend will present Boltz-2!
bit.ly/boltz2-pdf

Structure models and careful affinity data handling result in an affinity predictor approaching FEP accuracy at 1000x the speed.

Zoom link: portal.valencelabs.com/starklyspeak...

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Hannes Stark @hannes-stark.bsky.social · Jun 8

Tomorrow in our reading group we will discuss "Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functional" arxiv.org/abs/2504.18506

On zoom 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...

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Hannes Stark @hannes-stark.bsky.social · Jun 1

Reading group tomorrow: Identifying perturbation targets through causal differential networks arxiv.org/abs/2410.03380

With @menghua_wu!

Join us on Zoom at 9am PT 12pm ET 6pm CEST: portal.valencelabs.com/starklyspeak...

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Reposted by Hannes Stark

MIT Jameel Clinic @aihealthmit.bsky.social · May 28

📢 Thrilled to announce the return of MoML @ MIT on Oct. 22 and that paper submissions are now open! Students & postdocs w/ accepted papers will be granted FREE admission to attend and have the chance at winning the Octavian-Eugen Ganea Prize for Best Paper! 🧵 #AcademicSky #compchem #drugdesign

Graphic that reads "MoML @ MIT Call for Papers | 6th Molecular Machine Learning Conference" followed by smaller text that says "Topics of interest include but are not limited to: Geometric deep learning • Graph machine learning • Molecular dynamics • Structure prediction • Machine learning for quantum chemistry"At the bottom third of the graphic, the text reads "Deadline: Friday, Sept. 26, 2025 | Conference Date: Wednesday, Oct. 22, 2025 | Win a cash prize of $1,526 for Best Paper!"

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Hannes Stark @hannes-stark.bsky.social · May 25

Tomorrow @TimothyDuignan joins us to discuss "Orb-v3: atomistic simulation at scale" arxiv.org/abs/2504.06231 and surrounding models to get our understanding of that field up to date!

On Zoom 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...

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Hannes Stark @hannes-stark.bsky.social · May 18

Tomorrow the authors @YuanqiD and Jiajun He will present their paper "FEAT: Free energy Estimators with Adaptive Transport" arxiv.org/abs/2504.11516

Estimating FED is a strong tool for comparing drug's binding affinities

Join us on zoom at 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...

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Hannes Stark @hannes-stark.bsky.social · May 11

Reading group tomorrow: @json_yim and @woodyahern present "Atom level enzyme active site scaffolding using RFdiffusion2" www.biorxiv.org/content/10.1...

Join on Zoom at 9am PT / 12pm ET / 6pm CEST: portal.valencelabs.com/starklyspeak...

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Hannes Stark @hannes-stark.bsky.social · Apr 20

In the reading group sessions tomorrow Ezra Erives, I and whoever joins, will discuss "A General Framework for Inference-time Scaling and Steering of Diffusion Models" arxiv.org/abs/2501.06848

On zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg

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Hannes Stark @hannes-stark.bsky.social · Mar 23

Reading group session tomorrow, March 24th, is at 3pm PT / 6pm ET / midnight CEST about:

"One-step Diffusion Models with f-Divergence Distribution Matching" arxiv.org/abs/2502.15681
Presented by @xuyilun2

Zoom link: portal.valencelabs.com/logg

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Reposted by Hannes Stark

Hannah Wayment-Steele @hkws.bsky.social · Mar 20

Protein dynamics was the first research to enchant me >10yrs ago, but I left in PhD bc I couldn't find big experimental data to evaluate models.

Today w @ginaelnesr.bsky.social, I'm thrilled to share the big dynamics data I've been dreaming of, and the mdl we trained w them: Dyna-1.
📝: rb.gy/de5axp

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Reposted by Hannes Stark

Hani Goodarzi @genophoria.bsky.social · Mar 14

Check out this talk from our own Garyk Brixi talking about Evo 2!

Hannes Stark @hannes-stark.bsky.social · Mar 13

Video is up!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!

Genome modeling and design across all domains of life with Evo 2 | Garyk Brixi

YouTube video by Valence Labs

youtu.be

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Hannes Stark @hannes-stark.bsky.social · Mar 13

Video is up!
"Genome modeling and design across all domains of life with Evo 2" youtu.be/Rarn97Wpl1A
With the author Garyk Brixi!

Genome modeling and design across all domains of life with Evo 2 | Garyk Brixi

YouTube video by Valence Labs

youtu.be

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Reposted by Hannes Stark

Arne Schneuing @rne.bsky.social · Mar 7

The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available

📚 Paper: openreview.net/forum?id=g3V...

💻 Code: github.com/LPDI-EPFL/Dr...

(1/4)

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Reposted by Hannes Stark

Ilia Igashov @igashov.bsky.social · Mar 11

🚨 Check out DrugFlow, our new generative model for structure-based drug design. DrugFlow provides an atom-level confidence score for each designed molecule, and can adjust molecular size on the fly!

Additional details in thread 🧵

#ICLR2025

Arne Schneuing @rne.bsky.social · Mar 7

The code & camera-ready version of our #ICLR2025 paper on "Multi-domain Distribution Learning for De Novo Drug Design" are now available

📚 Paper: openreview.net/forum?id=g3V...

💻 Code: github.com/LPDI-EPFL/Dr...

(1/4)

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Reposted by Hannes Stark

Karsten Kreis @karstenkreis.bsky.social · Mar 11

🔥 ProtComposer (ICLR'25 Oral) is a Swiss Army knife:

(i) Manually create new protein structure layouts? ✅
(ii) Generation with favorable designability/diversity/novelty trade-offs? ✅
(iii) Spatially edit given proteins? ✅

Very original work by the amazing @hannes-stark.bsky.social and Bowen Jing!🔥

Hannes Stark @hannes-stark.bsky.social · Mar 10

New paper (and #ICLR2025 Oral :)):
ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids arxiv.org/abs/2503.05025

Condition on your 3D layout (of ellipsoids) to generate proteins like this or to get better designability/diversity/novelty tradeoffs.
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Hannes Stark @hannes-stark.bsky.social · Mar 10

Code: github.com/NVlabs/protc...
Humans:
Moi*, Bowen Jing*, Tomas Geffner, @jyim.bsky.social , Tommi Jaakkola, Arash Vahdat, @karstenkreis.bsky.social

Many of us will be at #ICLR2025 with this stuff, happy to chat!

Also happy to improve the NVIDIA logo a bit with this beauty made by Bowen🙃
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Hannes Stark @hannes-stark.bsky.social · Mar 10

Here are images of the rest of the figures because why not.
(we also have classifier free guidance between the conditional and the unconditional model to trade off ellipsoid adherence or to recover the original model)
5/6

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Hannes Stark @hannes-stark.bsky.social · Mar 10

Our ellipsoid generation model is a simple statistical model => not overfit on the data => produces novel and diverse ellispoid layouts => ProtComposer produces novel and diverse proteins => nice pareto frontiers of designability vs. diverisity/novelty/helicity
4/6

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